Hi, I have the package ComplexUpset as a dependency for some packages and the recent changes to ggplot2 v3.5.0 have thrown a spanner in the works. ComplexUpset calls `theme_minimal()` internally, but it appears that after updating to ggplot2 v3.5.0 locally this specific call is still returning values as for ggplot2 3.4.x which throws a build error for my packages, despite this being a direct call to the ggplot2 function theme_minimal(). I suspect that ComplexUpdate's call to theme_minmal() is somehow returning values from the version of ggplot2 that was installed at the time of it's own install. I uninstalled ComplexUpset locally and reinstalled it and this has fixed the error for me. The identical call is now returning values which are compatible with ggplot2 v3.5.0 As there are no package updates for ComplexUpset, I can't see this being resolved on the BBS any other way than a clean reinstall of ComplexUpset. Do complete reinstalls happen regularly, or are they only triggered by package updates? If the latter, is there a way of performing a manual reinstall of ComplexUpset on the BBS Sorry if that's a bit confusing. Please see https://github.com/krassowski/complex-upset/issues/195 for more details Thanks Stevie
[Bioc-devel] Build errors from recent breaking ggplot2 changes
3 messages · Stevie Pederson, Vincent Carey, Shepherd, Lori
thanks for the report, we will discuss this today. it should be possible to address this soon. On Tue, Feb 27, 2024 at 6:02?AM Stevie Pederson <
stephen.pederson.au at gmail.com> wrote:
Hi, I have the package ComplexUpset as a dependency for some packages and the recent changes to ggplot2 v3.5.0 have thrown a spanner in the works. ComplexUpset calls `theme_minimal()` internally, but it appears that after updating to ggplot2 v3.5.0 locally this specific call is still returning values as for ggplot2 3.4.x which throws a build error for my packages, despite this being a direct call to the ggplot2 function theme_minimal(). I suspect that ComplexUpdate's call to theme_minmal() is somehow returning values from the version of ggplot2 that was installed at the time of it's own install. I uninstalled ComplexUpset locally and reinstalled it and this has fixed the error for me. The identical call is now returning values which are compatible with ggplot2 v3.5.0 As there are no package updates for ComplexUpset, I can't see this being resolved on the BBS any other way than a clean reinstall of ComplexUpset. Do complete reinstalls happen regularly, or are they only triggered by package updates? If the latter, is there a way of performing a manual reinstall of ComplexUpset on the BBS Sorry if that's a bit confusing. Please see https://github.com/krassowski/complex-upset/issues/195 for more details Thanks Stevie [[alternative HTML version deleted]]
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We often don't like having to do a manual uninstall / reinstall of a package because that will not fix the issue for any typical user on their local system. It would be best to have complexupset bump there version so that everyone (universally) would get a fresh install. Hopefully they would consider this as well. Cheers, Lori Shepherd - Kern Bioconductor Core Team Roswell Park Comprehensive Cancer Center Department of Biostatistics & Bioinformatics Elm & Carlton Streets Buffalo, New York 14263
From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Vincent Carey <stvjc at channing.harvard.edu>
Sent: Tuesday, February 27, 2024 7:23 AM
To: Stevie Pederson <stephen.pederson.au at gmail.com>
Cc: bioc-devel <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Build errors from recent breaking ggplot2 changes
Sent: Tuesday, February 27, 2024 7:23 AM
To: Stevie Pederson <stephen.pederson.au at gmail.com>
Cc: bioc-devel <bioc-devel at r-project.org>
Subject: Re: [Bioc-devel] Build errors from recent breaking ggplot2 changes
thanks for the report, we will discuss this today. it should be possible to address this soon. On Tue, Feb 27, 2024 at 6:02?AM Stevie Pederson < stephen.pederson.au at gmail.com> wrote: > Hi, > > I have the package ComplexUpset as a dependency for some packages and the > recent changes to ggplot2 v3.5.0 have thrown a spanner in the works. > ComplexUpset calls `theme_minimal()` internally, but it appears that after > updating to ggplot2 v3.5.0 locally this specific call is still returning > values as for ggplot2 3.4.x which throws a build error for my packages, > despite this being a direct call to the ggplot2 function theme_minimal(). I > suspect that ComplexUpdate's call to theme_minmal() is somehow returning > values from the version of ggplot2 that was installed at the time of it's > own install. I uninstalled ComplexUpset locally and reinstalled it and this > has fixed the error for me. The identical call is now returning values > which are compatible with ggplot2 v3.5.0 > > As there are no package updates for ComplexUpset, I can't see this being > resolved on the BBS any other way than a clean reinstall of ComplexUpset. > Do complete reinstalls happen regularly, or are they only triggered by > package updates? If the latter, is there a way of performing a manual > reinstall of ComplexUpset on the BBS > > Sorry if that's a bit confusing. Please see > https://secure-web.cisco.com/1EJ2QRPcZds3ML76YRwBT1sib6spY2v5-pTuhDskor7QaqCVoniEapaHJQpbgzp0Ty3WGwimCdggeUaqz05dyliMRpOFlbJvaiTJTjeckPsWfpra21hWSTTcs9KzIqKCkGSLvSrRO_hXFkqxmpkYQZRq-KZvtgGmzcdbNRcIsjwUJwHOAELtfO1MSsh10-xIxdSYKlpsrARHKKD64Hq_16APXEEZSDOTg7pFFL-Jk6UyOB0StPJB0Pq-U0_5Wl2arHXNyb0Zmyb0ZAYVNJWowIFTdZ-QZGwt0sjdea_YLNi68ce6KrJZvMkulOhiRs4Qt/https%3A%2F%2Fgithub.com%2Fkrassowski%2Fcomplex-upset%2Fissues%2F195 for more details > > Thanks Stevie > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel at r-project.org mailing list > https://secure-web.cisco.com/1aD-BAZ5uwu4BKxND4PDlCN4a0v35aimNlYHB5vprr1EQB8N-amMfPFRE0IcYn5lbzdukvo9dlT3teH5F1yL--PBAlle6Bz_Rl1JFGM7T7K_-Ci-cFoSM-f_gXtd6K_bLR9sDcib9ZLeUZd5d2Xhc7g0Ramrm6aYWj6mryqToZZt3Zo-QMmMw2_RIBsO0huXC5gbDYP4nIT4YmceElEk37EPa4Z4wUShQSiF-jIt0ByXd8Gb2YlNudfZooB10cdcrcKMjVjllbH961cfQzJRf0vivrG-TgydxJB23t2-Dg5zVExxECXn9XlVmib49ZUce/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel > -- The information in this e-mail is intended only for the ...{{dropped:18}} _______________________________________________ Bioc-devel at r-project.org mailing list https://secure-web.cisco.com/1aD-BAZ5uwu4BKxND4PDlCN4a0v35aimNlYHB5vprr1EQB8N-amMfPFRE0IcYn5lbzdukvo9dlT3teH5F1yL--PBAlle6Bz_Rl1JFGM7T7K_-Ci-cFoSM-f_gXtd6K_bLR9sDcib9ZLeUZd5d2Xhc7g0Ramrm6aYWj6mryqToZZt3Zo-QMmMw2_RIBsO0huXC5gbDYP4nIT4YmceElEk37EPa4Z4wUShQSiF-jIt0ByXd8Gb2YlNudfZooB10cdcrcKMjVjllbH961cfQzJRf0vivrG-TgydxJB23t2-Dg5zVExxECXn9XlVmib49ZUce/https%3A%2F%2Fstat.ethz.ch%2Fmailman%2Flistinfo%2Fbioc-devel This email message may contain legally privileged and/or confidential information. If you are not the intended recipient(s), or the employee or agent responsible for the delivery of this message to the intended recipient(s), you are hereby notified that any disclosure, copying, distribution, or use of this email message is prohibited. If you have received this message in error, please notify the sender immediately by e-mail and delete this email message from your computer. Thank you.